Re: [Bkchem-user] Using BKChem as a library for generation of 2D structure images

[Beda Kosata]

You are right, OSRA (http://cactus.nci.nih.gov/osra/) is great, but my
library is called OASA (as in Obviously Another Stupid Acronym) :)))
Please let me know if you stumble upon anything strange. The library is
not very well organized and presently undergoes some changes (mainly
additions of functionality).
You might want to try the development sources:

tla register-archive http://bkchem.zirael.org/arch/2004
tla get -A address@hidden oasa--develop oasa

Beda

p.s.- please be warned that some of the code might be "write-only".

Noel O'Boyle wrote:
> OSRA looks perfect for the job (particularly example2.py). I will
> carry out some tests with it over the weekend.
> 
> Noel
> 
> On 27/03/2008, Beda Kosata <address@hidden> wrote:
>> Noel O'Boyle wrote:
>>  >
>>  > Hmm...it seems that it's necessary to start the Application. Do you
>>  > have any plans to separate some of the functionality into a library
>>  > that could be accessed without starting the App? For example, I simply
>>  > want to (1) build a molecule (using the information in the connection
>>  > table of a pybel molecule), (2) generate 2D layout, (3) create an
>>  > image (preferably stored in a string, rather than in a file).
>>
>>
>> The problem here is that the started App lets you measure exact (or
>>  almost exact) text size, thus enabling much nicer output.
>>  Also there is the whole machinery of the App behind you, so you can
>>  relatively easily work with color, fonts, etc.
>>  But its true that it is slow and ineffective.
>>
>>
>>  >
>>  > It would be great to have this as a library, not just for Pybel.
>>  > According to today's write up on Depth First, BKChem is one of only 4
>>  > available structure diagram generators...and the only one in Python
>>  > (see 
>> http://depth-first.com/articles/2008/03/26/five-open-tools-for-2d-structure-layout-aka-structure-diagram-generation)
>>  >
>>
>>
>> Interesting. The 2D coordinate generation is done in the OASA library I
>>  mentioned. This particular part of the library was written some 3 or 4
>>  years ago when I was doing a postdoc in Germany and had plenty of free
>>  time in the evenings. I did not touch the code since and it has some
>>  weak points (such as possible overlaps of atoms in highly branched
>>  structures), etc.
>>
>>  This brings us nicely to the second option I mentioned - using OASA (the
>>  library that is behind BKChem). I use it on http://inchi.info to
>>  generate pictures in the converter. It is not able to run without
>>  X-windows installed, because it uses cairo for picture generation and
>>  cairo does not work without X installed. However, you don't need X
>>  running. I use it for PNGs now, but cairo is capable of producing PDF's,
>>  EPS's and SVG's as well.
>>  I attach two  small scripts that demonstrate what you can do. Just copy
>>  it to the bkchem directory where the oasa library resides and run it. As
>>  you can see the OASA api is not that different from Pybel and it would
>>  be almost no effort to create a bridge between the two (as I intent to
>>  do in neat future :)
>>  The only problem here is that I did not put that much effort into the
>>  cairo output backend, so the result is not that nice. Also there is not
>>  much support for configuration of display options for atoms, fancy
>>  things like sub- and superscripts, etc. (In BKChem you can say "I want
>>  this atom rendered with symbol on and hydrogens on, I also want each
>>  nitrogen atom painted in green"; you cannot do this in OASA (without
>>  some hacking)).
>>  It all depends on what you need.
>>
>>
>>  > My other question is how stable is the BKChem API?
>>  >
>>
>>
>> Well, it depends. Some parts of the API are pretty stable, but I don't
>>  hesitate when I need to change something when I need to. I try to
>>  document changes in commit logs, but not very thoroughly because I am
>>  the only one working on BKChem.
>>  Maybe it is better to give an example - there are some batch scripts
>>  that I have created some two years ago that work even with recent
>>  versions. On the other hand there are a few that I had to tweak slightly
>>  because they used things that changed slightly over the time.
>>
>>  Best regards
>>
>>
>>         Beda
>>
>>
> 


-- 
Bedrich Kosata
Laboratory of Informatics and Chemistry
ICT Prague
Czech Republic

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